OBJECTIVES:  To examine the relationship between disease specific-measure, Health Assessment Questionnaire (HAQ) disability index (DI) and the preference-based measures, Short Form-6D (SF-6D) and the EuroQoL (EQ-5D) in patients with rheumatoid arthritis(RA) and psoriatic arthritis (PsA). METHODS:  Five hundred and four patients attending a rheumatology outpatient clinic with RA and PsA completed the HAQ, Short Form-36 and the EQ-5D before starting biologic therapy and 12 months after. The SF-36 was converted into a utility using the preference-based SF-6D. Clinical outcomes such European League Against Arthritis (EULAR) Disease Activity Score (DAS), joint counts and laboratory measures were also recorded. We calculated single index utility scores from the preference-based instruments using UK population norms. We used regression analysis and correlation coefficients to compare relationships between the Quality of Life (QoL) outcomes and also the clinical outcomes and between observed and mapped utility scores. RESULTS: There was a significant difference between the mapped and observed EQ-5D and SF-6D.  Overall the mapped utilities produced higher values than the actual observed scores. The mean change in utility due to treatment is greater with the EQ-5D for both mapped and observed utilities. A greater change was seen in the PsA group.   CONCLUSIONS: We present the different results produced when using mapped utility scores and directly obtained scores. We have highlighted the problems associated with deriving utilities from non preference-based instruments and the differences in utilities when calculated using different measures. While these methods do offer alternatives for researchers when performing cost utility analysis they remain suboptimal to the direct method.